Cell Biology Python Packages

cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

deepcell

Deep Learning Library for Single Cell Analysis

cellsepi

A modular platform for end-to-end batch cell segmentation and quantification for microscopy images.

cellpyability

Software for the automated analysis of in cellulo high-throughput drug screening

deepliif

Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]

pyvertexmodel

3D vertex model allowing scutoids

cello-classify

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

deepcell-cpu

Deep Learning Library for Single Cell Analysis

cellshape

3D shape analysis using deep learning

epitools

Quantifying 2D cell shape and epithelial tissue dynamics

u-segment3d

Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method.

napari-pyvertexmodel

Napari plugin to run 3D vertex model

actk

Automated Cell Toolkit

cellpose-mcp

MCP tools for Cellpose and napari integration

biosimulations-bigg

Command-line program and scheduled GitHub action for publishing the BiGG model repository to BioSimulations

biosimulators-rbapy

RBApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

deepcelltl

Deep Learning Library for Single Cell Analysis

napari-vesicles-segmentation

A simple plugin to detect vesicles in cells images.

cellpose-vollseg

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

cellgeometry

A web-based application for Cell Shape Analysis.

spheroidpy

Python Package for the Analysis of Spheroid Microcopy Data

u-unwrap

Map complex and diverse 2D cell shapes into canonical disk and rectangular coordinate systems for streamlined analysis including spatiotemporal registration, windowing and machine learning. Also supports 2D contour-guided remapping and windowing. 2D analogous package to our 3D version, u-Unwrap3D.

u-unwrap3d

Transform 3D cell surfaces into different representations including topographic maps, 3D spheres, and 2D images for doing optimized quantification, data analysis and machine learning.

optiflow

Reconstruction of flows from kymographs with optimal transport